It was founded in 1614 at the behest of Anna Fastkowska and Anna Poradowska for girls from noble families. After the Partition of Poland the Austrian administration decided to secularise the convent. In 1784 the Brygidki building was turned into a prison, where death sentences would be carried out on a regular basis until the 1980s.

Taken over by the Soviet Union after Soviet invasion of Poland in 1939, the prison was one of three sites of mass murder of political prisoners by NKVD in Ukraine in June 1941 as the Soviets were retreating before the Nazi German invasion. Approximately 7,000 prisoners - primarily Poles and Ukrainians - died in Lviv in that event.

Amongst those who perished on June 30, 1941, was Fr. Zynoviy Kovalyk, whom the NKVD arrested in December for the sermon he gave on the Feast of the Immaculate Conception (December 8). While they shot the rest of the prisoners, they decided to treat Fr. Kovalyk like his Lord by crucifying him in front of his fellow prisoners. When German troops had conquered Lviv, many people hastened to the prison in the hope of finding their relatives. According to witnesses, the most terrible sight was that of seeing the priest nailed to the prison wall. Even worse, someone had slit his belly open and placed a dead human fetus inside of it.